Shadow the Hedgehog 2
by DisjointWinter
Summary: With the Black Arms invasion still fresh in everyone's mind, a new tragedy and mystery unfolds, and the ultimate life form is, once again, the Earth's only hope. R
1. The Faceoff

Shadow the Hedgehog 2

Chapter 1: The Face-off

_Sonic_

_Meet me at Westopolis. Bring Tails, Knuckles, Amy, Rouge, and a video camera. Be at the center of the city at noon. Be ready to fight for your life._

Sonic looked at the note, puzzled, as he and his friends walked through the ruins of Westopoils. It was one of the many cities still in ruins from the Black Arms attack.

"Any idea who sent the note, Sonic?" asked Tails who was holding the camera.

"Not a clue, buddy." Sonic answered.

"I bet it was that creep, Eggman!" shouted Knuckles.

"Why would he want most of his strongest enemies to come to him, ready for anything?" asked Rouge.

Knuckles said nothing.

"This place gives me the creeps!" yelled Amy while holding on to Sonic's arm.

"There's nothing to be scared of, Ames," Sonic said, trying to keep Amy calm. "I won't let anything hurt you."

"It's not me I'm worried about," Amy said, burying her face in Sonic's chest. "It's you."

"Why would you-" Sonic started.

"I fell like..." Amy interrupted. "Like I'll never see you again after this." Amy started to cry.

"Come on Amy, I'll be fine." Sonic said in a vain attempt to calm Amy down, but she kept crying. '_Man, she's really upset_.' Sonic thought as he started to stroke Amy's quills. Recently, Sonic had begun to care deeply for the pink hedgehog. "Shh, shh, Amy, I'll always be here for you."

Amy looked up at Sonic. "You promise?"

Sonic looked at her, smiled softly, and kissed her forehead. "I promise."

"Hey Sonic, stop flirting with your girlfriend!" Yelled Knuckles. "We're here." He pointed to a large fountain that marked the center of the city.

Had Amy not been crying, Sonic would have cussed Knuckles out or yelled "She's not my girlfriend!" but Sonic didn't want to upset her more than she already was.

"Hey Tails, what time is it?" asked Sonic.

Tails checked his watch. "11:59, what ever is going to happen should be starting soon."

And it did. Suddenly, there was a flash of red light. When the light faded, a black figure with glowing crimson eyes and a big evil grin stood in front of the fountain, ten yards away from our heroes. He was wearing a red jacket and red jeans.

"Shadow!" cried our heroes.

Shadow chuckled evilly. "Hello everyone."

"Shadow, was it you who sent the note to Sonic?" asked Rouge. Shadow nodded. "Why?"

Shadow's grin broadened. "Because, I want to do something with Sonic, something I can't do in an over populated area."

Sonic stepped forward his brow arced in confusion. "And just what might that be?"

"I want to fight you." Shadow said in voice of pure excitement, highly unusual for the dark hedgehog.

Sonic's eyes widened. "Fight me, huh? But then-"

"I want there to be documented proof and eye witnesses to your defeat, so that no one will dare question who the most powerful hedgehog in the world is!" Shadow shouted the answer to Sonic's question before he could ask it.

Sonic grinned. "You thought this through, huh? Tails," He looked back at twin-tailed fox. "You rolling, buddy?"

Tails quickly turned on the camera and pointed it at Sonic and Shadow. "Rolling!"

"Alright than, Sonic, defend you're self!"

Shadow started skating towards Sonic, who had begun to run at him. They meant in about half of a second and began punching, kicking and dodging each other at speeds so great that they appeared to be just a black and a blue blur.

Sonic tried to punch Shadow in the head, but, Shadow dodged it by ducking down. Taking the opportunity, Shadow gave Sonic a kick to the jaw, sending him flying upwards.

When he was about ten stories up, Shadow Chaos Controlled in front of him and began to hit him with a barrage of powerful punches before grabbing his left ear to spin then throw Sonic into a nearby building. Sonic flew through two buildings before coming to a stop half way through the third.

The blue blur dragged himself out of the rubble, coughed up a little blood and stood up. '_Man, it feels like I just got in a wrestling with a monster truck and lost, Shadow's not playing around, if I don't take him seriously I might get myself killed_.' Sonic walked over to the hole he made in the building when Shadow throw him through it and looked out to see Shadow standing at the exit hole in the second building Sonic flew through.

Shadow still had an evil grin on his on his face and his eyes were still glowing. He stared down at Sonic. "What's the matter faker, don't tell that's all you got!"

Sonic's lips twisted into a smug grin. "Heh, not even close, hate to be the one to tell you this, but, you're goin' down!" He gave Shadow a thumbs-down.

Shadow shook his head. '_Wrong, Sonic_,' thought Shadow. '_You're the one who's going down, six feet underground to be exact_.'

Shadow jumped into a Homing Attack aimed at Sonic, who did the same. The two hit, were bounced back and tried again. After about ten attacks, Sonic finally got the upper hand blasting Shadow into the wall of a nearby building, but not through it. Sonic tried to hit Shadow with another Homing Attack, but Shadow used Chaos Control to warp away just before he hit. Sonic ended up crashing almost all the through the building.

Sonic laid faced down inside the ruined building, he sat up and started shaking and grabbing his head. '_Damn it Shadow!'_Sonic screamed in his head._'How can I beat him if he keeps using Chaos Control_?' Sonic sat there thinking about it. '_If only I had a Chaos Emerald that would even the odds a bit_.'

Sonic continued to think of this until he noticed something glowing under some nearby rubble. Moving over to it, Sonic realized what it was and quickly began to dig it out.

"Yes!" Sonic yelled for joy as he held the light blue Chaos Emerald. "Man talk about luck!"

"Yeah, talk about luck." Sonic turned to see Shadow about to give him a good punch to the head.

Sonic held on to the Emerald for dear life and yelled "Chaos Control!"

Shadow's fist made a nice hole in the floor, but Sonic had disappeared. Sonic reappeared behind Shadow, giving him a good kick to the back of the head that sent him flying out of the building and into the one across the street.

Shadow burst out of the rubble and move to the hole he made. Across the street, Sonic stood at Shadow's exit hole, a smile of pride on his face.

Shadow glared at the cobalt hero, and said "So, Sonic, now you have an Emerald?"

"That's right Shadow, I think this evens the odds!" Sonic replied as he flashed Shadow a toothy grin.

"You think so? Well I'll still win! And you will die." Shadow whispered the last part. "Now, let the real battle begin!"


	2. Sonic Dethroned

Chapter 2: Sonic Dethroned!

The battle had been going for a good six hours. Much of the city had been destroyed by the two hedgehogs throwing each other through them.

Due to the distance, Tails had to fly to the top of a nearby building to get even a glimpse of the rivals, going too close would be suicide after all.

In the distance, another building came crumbling down. '_Man, this is intense_,' thought the twin-tailed fox, '_glad I brought an eight-hour type_!"

"_Hey Tails!_" came Knuckles' voice over Tails' walkie-talkie. "_Can you see who's winning?_"

Tails put his walkie-talkie near his head and replied. "Sorry Knuckles, I can't even see them."

Knuckles threw the walkie-talkie on the ground, nearly breaking it. "Man, I can't take much more of this!" yelled the enraged echidna, "I want to know how badly Sonic's beating Shadow!"

Rouge narrowed her eyes at him. "What in that red little head of yours makes you think Sonic has a chance of winning?" she asked. "Shadow has more superpowers, more strength and more stamina than ten Sonics!"

Knuckles wheeled around and glared at the ivory huntress. "Oh, shut it, Rouge!" spat the guardian, "Sonic's way faster than Shadow and you know it!"

The bat stormed up to Knuckles and yelled, "So?"

"Strength means nothing if you can't hit your opponent!" Knuckles rubbed his chin before adding "I learned that first hand."

Rouge rolled her eyes. "_Speed_ means nothing if your opponent can stop time!"

Knuckles' left eye twitched, he was unable to argue with that. After a moment, the guardian just screamed, "Fine, but Sonic'll still win!"

"No, Shadow will!"

"Sonic!"

"Shadow!"

"SONIC!"

"SHADOW!"

While Rouge and Knuckles continued their argument, Amy just stared at where the battle was being fought, praying for Sonic's safe return. '_He'll be fine_.' thought Amy. '_He has to be fine, he promised_.'

Bruised, bleeding, panting heavily and clutching his emerald close to his heart, Sonic stood with his back pressed against a pile of rubble that was once a wall of a business building. '_This is crazy_!' thought Sonic. '_I ready to pass out and I don't think Shadow's even hurt yet_!'

Than Sonic heard something that made his heart skip a beat, footsteps, growing louder and louder before stopping right behind him. Sonic held his breath, he knew what would happen if he made a sound.

"Sonic," came Shadow's voice from the other side of the rubble. "Sssooonnnic, come ooooout."

'_Is he_,' thought Sonic. '_Is he singing_?'

"Sssooonnniiic, where are yooouuu?" Sonic heard footsteps again and let out a sigh, which Shadow heard and stopped. "Found you Sonic!" In Shadow's hand a ball of energy appeared. He pointed this energy at the pile of rubble. "Say good bye, Sonic! Chaos Cannon!"

The ball of energy grew to twice Shadow's size and went flying at the wall of rubble. It burst through in less than a second, hitting Sonic from behind, causing him to drop his emerald and sending him flying thorough one and a half buildings before exploding in the second building sending him flying in to the street and demolished the building. Sonic laid face down in the street and didn't want to get up.

"That's it!" said Sonic as he got to his feet. "I give up! There's no way in hell I can beat Shadow now!" He looked down the street and saw the fountain where his friends were waiting. He started walking towards it when he heard someone whistle behind him.

Sonic turned around to see another Chaos Cannon fly right into his face. This one exploded the moment it hit him sending him flying back towards and thorough the fountain before stopping on a pile of rubble with his friends to his right.

"Sonic!" yelled Tails as he landed. When he was on the ground everyone started running towards Sonic but stopped when Shadow appeared in front of him. Shadow's arms were crossed, his grin had faded but his eyes were still glowing.

Sonic looked up at the black hedgehog and laugh nervously. "Heh, man Shadow." said Sonic. "Didn't think you had it in ya." He raised his right hand to Shadow. "You win buddy, you really are the best!" Shadow reached out his right hand as well, but not to shake Sonic's, for in Shadow's hand was a handgun aimed right at Sonic's heart. "Shadow, w-w-w-what are you d-d-d-doing?"

"Game over, Sonic" said Shadow as he pulled the trigger. The gun went off and Sonic was in immediate pain and move his left hand in a desperate attempt to stop the bleeding. Shadow turned and began to walk with a grin of pride on his face as he whispered "Phase 1 complete, Doctor."

All of Sonic's friends gathered around him, Amy had started crying as she dropped to her knees right next to Sonic, his eyes were closed. "Sonic, Sonic! Say something!" said Amy thorough her tears. "Sonic, you promised, you said you'd be alright! Say something you lair!"

"Amy." said Sonic weakly. "You there?" He slowly opened his eyes.

"Yes Sonic, I'm here!"

Sonic looked up at her. "Amy, there's something I have to tell you." He raised his right hand up and Amy grabbed it with both hands.

"What is it?"

"Amy, I... I... I..." Sonic's eyes closed and his head went limp. Amy let go of Sonic's hand and it fell to the ground.

Everyone just stood there, the reality of the situation slowly sinking in. When it did, Amy immediately burst into uncontrollable sobs as tears poured down her face, Tails did the same soon after, Rouge just stood there with a look of shook on her face and Knuckles began to cry, but his sadness quickly turned to rage, rage he would take out on the hedgehog who had done this unforgivable crime.

Knuckles looked around and saw Shadow slowly skating away and ran after him. '_You bastard_.' thought Knuckles. '_You'll pay! I swear I'll kill you, Shadow the Hedgehog_!'


	3. Scarlet the Hedgehog

Chapter 3: Scarlet the Hedgehog

Knuckles continued to chase Shadow out of the ruined city. The chase was now thorough the forest outside of Westopoils. Had he not been so focused on killing Shadow, Knuckles might have found it strange that Shadow had not used Chaos Control to leave the battlefield, but instead skated away slow enough for Knuckles to follow, without having to strain himself. But Knuckles probably won't have care, even if he had noticed.

Shadow skated up a hill and stopped at the top, with Knuckles right behind. All of a sudden, there was a flash of red light, a gun went off and Knuckles was on his knees, grabbing a gun wound on his left arm. He looked up and saw Shadow holding in his left hand the gun that had shot him and just a few moments ago had killed Sonic.

Again, had Knuckles not been so focused on revenge he might had found the look of shook on Shadow's face odd, and the fact that his eyes were no longer glowing might have been noted, and maybe the greatest difference, the fact that Shadow was now wearing black jeans with a leather jacket would've been seen, but no, Knuckles didn't care.

"Knuckles! Did you-" Shadow began.

Before he could finish, Knuckles ran up and gave Shadow right punch to the face, a left to the gut, and one more right to the face. Shadow fell to the ground, looked up at Knuckles and passed out.

With a groan, Shadow awoke. He tried to move, but could not. Shadow looked at his arms, he was shackled by rings of glowing energy that made it impossible to move. He looked around only to see darkness everywhere.

_'Where's a light when you need one?' _thought Shadow. Then, as if activated by his thoughts, a bright light shined in front of him. When his eyes adjusted Shadow realized the light was coming from a large T.V. screen. On it was a side view Sonic lying on a pile of rubble with Shadow standing in front of him, aiming a gun at his heart. The Shadow on the screen said "Game over, Sonic" and pulled the trigger. Then the screen went black.

Shadow blinked as his mind tried to fathom what he just saw. "What the hell is going on?" he said at length.

"Does a number on a guilty conscience, doesn't it?" came a voice from the darkness. The lights on the celling went on to revile the voice came from the G.U.N. Commander, who stood in the front-left corner of the room.

The room was very large, at least thirty feet height and forty feet wide, the wall in front of Shadow was just two huge doors, there was a smaller door on the left wall, all four walls were grey and had white G.U.N. symbols on them, the machine the held Shadow took up half of the room and was shaped like a pyramid, with Shadow at the top.

The Commander took a few steps forward and rubbed his forehead. "You know Shadow, I'm willing to admit when I'm wrong. And I thought I was wrong about you."

Shadow's eyes narrowed at the old man. "What are you babbling about?" he asked angrily.

"This!" The Commander took out a remote, pointed at the screen and pressed on of its buttons, which caused the screen to once again show Shadow shooting Sonic. "I thought I was wrong when I said you were evil, but I was right! You murder one of this world's greatest heroes just to prove you were better, you devil!"

"What are you talking about? I'd never-" Before Shadow could finished the Commander pointed his remote at the machine holding Shadow and pressed another button which made it send thousands of volts of electricity thorough Shadow's body causing him to twitch and yell out in pain. After about thirty seconds of this torture, the Commander turned off the electricity. Shadow nearly passed out and found it difficult to stop twitching every few seconds.

"Don't even try to lie!" barked the Commander. "I have four witnesses and a video tape all saying you killed Sonic! And, as if that wasn't enough, you were holding the murder weapon when we captured you!" The Commander began walking to towards the smaller door, looked back and said "When I leave this room again, there will be one less monster in the world!" Then, he stormed out.

After walking down the hallway on the other side of the door and up the stairs, the Commander entered a room with thirty monitors, ten of which showed different views of the room Shadow was in, the rest showed different parts of the complex. From these monitors, it is obvious that this complex was Prison Island. There were ten G.U.N. operatives working on computers in the room. Also, in this room were Knuckles and Tails. Knuckles was looking at the monitors that showed Shadow with his fist clenched, while Tails just stood there with his head down.

"Man," started Tails, "I can't believe this is happening."

"Well it is!" barked Knuckles. He turned to the Commander and added "I say we make Shadow suffer for what he's done!"

A grim smirk appeared on the old man's face as he starred at Shadow on the monitors. "Nothing would make me happier." he said.

A G.U.N. solider entered the room. "Sir! Someone is here to speak with you." said the solider.

"Who ever it is, they can wait," the Commander answered without even turning around.

"But sir, it's the President and he's in the room."

The Commander turned around and saw the President was indeed in the room. Quickly, the Commander saluted him. "Mr. President, I didn't think you be coming here!"

The President eyed the Commander for a moment. "When one of our  
greatest heroes kills another, of course I'm going to get involved," he said darkly before turning to Shadow's monitors. "Now, were you really planning on killing Shadow right  
away?"

"Well ,sir, I-" the Commander started.

"He should be killed!" interrupted Knuckles. "He murdered Sonic and we have all the proof we need, so let's just finish him!"

"Well, I'm not satisfied," said the President. It's to my understanding that Sonic had accepted  
defeat. If that was the case, why would Shadow kill him? Especially when he  
knew that there would be proof incriminating him that would cause legal forces  
to take action against him"

"Sir," started the Commander. "What are you getting at?"

The President rubbed his eyes. "I just think more is happening here than we know."

Just then the ten monitors that showed Shadow went black. "Sir!" said one of the G.U.N. operatives. "We've lost all video feed form Containment Area 24!"

"Sir!" said another operative. "There's been a massive spike in Chaos Energy in Containment Area 24; I think someone has entered the room using Chaos Control!"

"Damn!" yelled the Commander. "That devil had an accomplice!" He took out a small communicator from his pocket. "Attention, all available units are to converge on Containment Area 24! I want all battle-mech units fully armed and ready to fight five minutes ago!"

Within minutes, almost every G.U.N. solider and mech on the island were in front of the large doors that lead to the room Shadow has held in, Containment Area 24, with Knuckles in front of them.

'_Alright Shadow_,' thought Knuckles. '_Time to pay_!'

Then there was a large explosion from inside the room that created a gap in between doors. In the gap, a black figure could be seen.

* * *

The Commander stormed out of the room, leaving Shadow hurt and confused.

_'Sonic's dead?' _thought Shadow. '_And everyone thinks I killed him! What the hell's going on?' _Shadow stood there trying in vain to figure it out, when a thought came to his mind. _'That hedgehog... that hedgehog with the glowing eyes! He said that he...'_

_Flashback_

_Shadow stood atop a hill out side Westopoils with his eyes closed and arms crossed._

_'Damn it all.' thought Shadow. 'Where the hell is the Doctor. He said to be here at 6:00 p.m., and he's no where to be found. What's this surprise he promised anyway?'_

_Shadow felt something hit his left foot. He looked down to see a handgun next to his foot, which he picked up and than turned around to see who threw it at him. What he saw was defiantly a surprise._

_'It's like looking in a mirror!' Shadow thought, and it was. The hedgehog in front of him looked just like him, except this one had glowing eyes and wasn't wearing anything but his natural fur._

_"That's a nice gun, huh?" said the other Shadow, his voice filled with pride. "It's the one I just used to kill Sonic the Hedgehog."_

_Shadow's eyes widened. "What?" he yelped in shook. "Who are you?" The other Shadow said nothing, which enraged the first. "Answer me!" Shadow shot the gun at his mirror image, who vanished in a flash of red light._

_Shadow ran to where his copy once stood and looked around. He then saw Knuckles on his knees holding his left arm._

_"Knuckles! Did you-" Shadow began, but couldn't finish because Knuckles attacked him and knocked him out._

_End of flashback_

_'... killed Sonic. That's it! He's the one who ended the faker.' _Shadow straggled to break free, but to no avail. '_I have to tell them who it really was!' _Realizing he could not use brute strength to escape, the ebony one calmed himself and tried to think of another way out.

Just then Shadow heard ten small explosions all around him. After which, a flash of red light came in front of the machine that held him. When it was over, the glowing eyed Shadow stood there.

After getting over the initial shock, Shadow stared hatefully at his twin. "You," he said. "Are you enjoying seeing me like this?"

The other Shadow chuckled as he said "More than you could ever imagine." He then jumped on to the machine that held the real Shadow. Their two faces were mere inches apart.

Further annoyed by how close he was to his copy, Shadow angrily asked, "Just who are you?"

The other Shadow chuckled evilly. "I'm the true Ultimate Life form! You're just a prototype compared to me!" He began to change. His black fur turned red, his red stripes turned black, his white chest fur turned yellow, his eyes stopped glowing and turned black. "I am Scarlet the Hedgehog!"

"Scarlet the Hedgehog?"

"That's right."

"You killed that faker!"

"Yep."

"And framed me?"

"Nothing gets past you, does it?"

"WHY!"

"Now, that would be telling."

"You smug, son of a bitch!"

Scarlet chuckled. "My mother is quite the pathetic man, isn't he?"

Shadow growled, annoyed further by his twin's lack of logic. "You'll pay..." Shadow said as he began to glow red. "You'll pay!" A red ball of energy grew around him. "YOU'LL PAY!"

Scarlet then vanished in a flash of red light, but Shadow continued on with his attack, ready to get out of this prison.

"CHAOS BLAST!" The ball of energy expanded with unbelievable force and speed, completely destroying the machine and created a gap in the doors. Shadow, who now stood in front of the ajar door, rolled his shoulders and cracked his neck.

_'No one shackles me,'_ Shadow growled inwardly. He then heard what sounded like of hundreds of soldiers and meches on the other side of the doors._ 'Right now they'll never believe me. I have to get out of here and catch Scarlet if I want to clear my name. Best way to do that,' _The dark hedgehog braced himself and shouted "Chaos Control!'

Shadow flicked for a second, but did not vanish. "What the hell?" He looked at the ruined machine behind him. _'That damn thing must have drained most of my energy and the Chaos Blast took what ever I had left. I'll need an Emerald to get out of here.'_ Shadow looked back at the door. _'As much as I love killing humans, that would only help my mood, not my case, so...'_

Shadow skated out the gap and past Knuckles, who tried to give him another punch, but Shadow was moving so fast he was just a blur.

The ultimate life form zigzagged through the soldiers, a few of which tried to shot him, only to succeed in killing the soldiers that was in front of them and making Shadow laugh. The meches weren't much more of a challenge, all he had to do was skate between their legs.

"Pathetic humans." said Shadow when he was through the "elite" forces of G.U.N. and heading for a large gate which he hoped lead to an exit. Shadow smashed the gate and found himself falling. He landed on a large square platform that had the length of a football field, was grey with a white G.U.N. symbol in the center, and was over something that had a blue glow. Shadow looked around for an exit; there wasn't one.

Then a large circular vehicle floated down from the celling. It was grey with several rocket launchers around it as well as on under the cockpit. It was piloted by a single G.U.N. solider. "Commander!" said the pilot to the radio. "This is the P.B.C.U. (Particle Beam Cannon Unit) leader Blue Falcon! I've spotted Shadow, preparing to engage the hedgehog!"

"Roger, Blue Falcon!" came the Commander's voice over the radio. "You are to stop Shadow at all costs, understood?"

"Yes sir! Get ready Shadow!"

Shadow crossed his arms, closed his eyes, and shook his head. "You humans don't know when to quit, do you?" Shadow struck a fight pose. "Humph. Let's get this over with."

The Blue Falcon began to circle the room, launching rockets at Shadow, which he could have easily dodged, but instead he grabbed one and threw it back at the Blue Falcon, causing noticeable damage to its weapons systems. Then, Shadow jumped into a homing attack, knocking of one of the Blue Falcon's rocket launchers.

Shadow was in the air above the vehicle when he felt a bit of his power return. With a smirk, he raised his hand in the air and shouted "Now to end this, Chaos Spear!" He quickly wave his hand and three energy projectiles were launched at high speeds at the vehicle. They hit and went straight thorough. The vehicle began to move madly.

"Damage to maim fuel tanks," said the pilot. "Massive damage to particle beam cannon and Emerald storage!"

"Emerald storage?" said Shadow as he landed on the Blue Falcon's back. "A Chaos Emerald?" He jumped and began another homing attack, which sent him straight thorough the Blue Falcon. When he came out the other side he was holding the blue Chaos Emerald. "Now we're talking!" Shadow turned around when he heard an explosion. He saw the Blue Falcon crash to the ground in a flaming heap of scrap metal.

Shadow sighed. "I guess I should save the pilot; I don't want G.U.N. to have any more ammo against me." He skated into the flames, pulled out the pilot, and got him away from the damaged vehicle. Shadow checked the man's vital signs, he was out cold, but still alive.

"Blue Falcon!" came the Commander's voice from the pilot's earpiece. "Blue Falcon, come in! Answer me damn it!"

Shadow took the earpiece from the pilot. "Hope the Blue Falcon wasn't very expensive," said Shadow to the earpiece. "Because now it's just scrap metal!"

"Shadow?"

"You should get medic up here. The pilot's not looking to good."

"Shadow you son of a bitch!"

"Now listen Commander, you and your soldiers are to leave me alone, got it? I'm not the one who killed that faker, if I was, I would have used my bear hands."

"You can't fool me, Shadow."

"You just don't like to listen, do you?" Shadow crushed the earpiece in his hand then looked at his Emerald. While looking at the Emerald, Shadow felt compelled to go to the ARK. "The ARK it is." Shadow held the Emerald over his head. "Chaos Control!" Shadow vanished.

Little did Shadow know that what he'd find on the ARK would change his life, forever


	4. Secrets Revealed

**Chapter 4: Secrets Revealed**

An empty, metallic hall, out the windows the Earth could be seen. Suddenly a flash of blue light fills the hall. When it ended Shadow stood in the hallway. He walked over to the window and looked out.

'_Yeah, this is the ARK,' _Shadow thought. '_Now, what am I here for?' _Shadow looked down the hall. '_I need to figure out what I'm here for before I get detected. Taking out any soldiers that come for me would be easy, but the more I do that; the less chance I have to clear my name._' Shadow began skating down the hall look for what compelled him to return here.

While skating, the dark hedgehog's mind raced in a vain attempt to figure out what was happening; Scarlet had killed Sonic and framed Shadow that much he knew, but why? Did Scarlet have some sort of grudge against the ebony one, or was he just trying to show off, what was he anyway?

For a moment, Shadow's thoughts turned to Scourge, the green hedgehog and Sonic's counterpart from a different dimension. Apparently, Scourge's home world, which was a mirror image of Sonic and Shadow's, himself being Sonic's twin, had been destroyed, how is unknown, and the hedgehog who would become Scourge was the only survivor. He ended up in Blaze's home dimension and quickly started to cause trouble. He ailed himself with Eggman Nega and tried to steal the Sol Emeralds.

The insuring chaos and energy release from the Emeralds resulted in Blaze, Eggman Nega, and the hedgehog being brought to Shadow's world. The hedgehog that would become Scourge fooled many into believing he was the real Sonic. After some confusion, the two Sonics had a showdown on Angel Island. While there, the evil Sonic absorbed a great deal of energy from the Master Emerald which greatly increased his strength, at the cost of some speed, and caused his eyes and fur to changed colors. He than changed his name to Scourge the hedgehog. Even with Nega's help, however, Sonic and Blaze were able to defeat him. Nega was taken back to Blaze's world to stand trail, while Scourge managed to escape and had not been heard from since.

Could that be what Scarlet was: Shadow's counterpart from Scourge's strange world, warped by the Master Emerald or its counterpart from a different world? That would explain a few things, but not his, apparent, vendetta against Shadow.

The ebony hedgehog shock his head; clearly, there were still too many missing pieces for Shadow to see the whole picture. Instead, he decided to focus on finding what compelled him to the ARK and save Scarlet for later.

* * *

Rouge sat on a couch in the living room of her mansion, with a look of disbelief and horror on her face.

'_Shadow_,' thought the bat. '_How could you do something like this? They're going to kill you now_.' Rouge shuddered at this thought; Shadow was one of the few people she could act like herself around. The other was a machine.

Then, the mansion's doorbell rang once.

A second time.

And a third.

Annoyed Rouge got up slowly and walked to the door. "Who's there?" she asked upon reaching it.

An all too familiar voice replied "It's me."

In an instant, Rouge ripped open the door to reveal Shadow, eyes glowing and leaning against the door frame with a hand covering a red spot on his left side.

"Shadow!" yelped Rouge in shook. "What are you doing here?"

"I... need... your... help," the ultimate life form said between heavy breathes.

Rouge stared at him from a while before shaking her head. "Why did you do it Shadow?" she asked

"I don't know... I just got caught up in the moment, you have to help me!"

Rouge took a few steps back. "Shadow, you have to turn yourself in!"

Shadow fell to his knees. "If I do that they kill me." He looked up at Rouge. "For the first time in my life, I'm scared." Shadow raised his hand to Rouge. "Please, help me."

Rouge hesitated for a moment, then took Shadow's hand.

* * *

Following a strange feeling he had, Shadow skated down the dark halls of the ARK until he reached a door with a plaque "Prof. Gerald Robotnik" on it. On the wall next to the door was a scanner clearly meant to scan someone's hand in order to open the door. Not sure if it would recognize his hand, Shadow opted to simply break the door down. One swift kick and he was in.

The darkened interior of the room was like most room on the A.R.K.; small, cold, and metallic. In the center of the room was a desk with a computer on top of it. Shadow walked over the desk and turn on the computer. The screen lit up and displayed box asking for a password. The ebony hedgehog rolled his eyes and typed in "Maria". The box on the screen disappeared and the desktop loaded up; a plain blue background dotted by several program shortcuts.

One icon caught Shadow's attention; a document entitled "Project Shadow". The dark hedgehog stared at the icon for a long time, mentally debating weather or not to open it. On one hand, he fought a small war to find out about his past and this document could hold every secret and every answer he wanted. On the other, Shadow had put the past behind him and this document could renew his hatred of humanity. Still, information on Scarlet maybe hidden within it. However...

'_Enough!_' Shadow screamed in his head, '_I'm opening the damn thing!_'

The ebony hedgehog took hold of the mouse and clicked the icon twice. After a moment, the document opened. It read:

_**Project Shadow**_

___(Formally known as Project Ultimate Life Form)_

_3/25/49: The government has grown impatient after the failure of the Biolizard. There is talk of shutting down not only my research team, but the ARK itself! They want a miracle, but refuse to give us the time or the resources to do it! I was going to tell that military blow-heart "General" Howerson what I thought of him, but then I ran into Maria. We had lovely talk and after that I didn't care about Howerson, or the government; I am here to make sure that she makes it out of grade school and I will do just that. N.I.D.S. is problem like any other and there is no problem that a Robotnik cannot solve!_

_4/8/49: Howerson was on my ass again today, complaining about the lack of progress and how unfocused the other scientists were. I told him that they would focus on their work more if he wasn't constantly hovering over them. "Just doing my job as overseer" he said. Bull! More like trying to see if we made anything worth weaponizing! I don't know how much more of him I can take!_

_The Black Comet will be passing by Earth soon. I remember seeing it as a boy with my grandparents. Maria and I are going to watch it when it comes. I swear, this maybe the last time I see it, but it will not be her last time!_

_4/10/49: I... I don't quite know how to put this, but I have just made contact with an extra-terrestrial! He... she... it... I am not sure of the gender, but it was humanoid with pitch black skin and red streak on its arms, legs and head. It claimed to be an emissary of one Black Doom, a rather ominous name now that I think about, who was the leader of the Black Arms, a race of aliens that inhabit the Black Comet! Just yesterday, Maria and I were on the Observation Deck watching that very same comet and I had no idea! The creature said that Doom knew about my research and wanted to help. I asked the creature why, but it said that Doom would explain everything. I will meet with this mysterious being tomorrow._

_4/11/49: I meant Black Doom today and let me just say, the name fits him quite well; he is utterly terrifying. Regardless, Doom offered me a deal; he would provide me with the D.N.A. of an immortal creature in exchange for a solider capable of quickly collecting the Chaos Emeralds. I always thought the Emeralds were just a myth, but Doom is convinced they are real. He has given me until tomorrow to decide. I will not lie, Doom reminds me a bit too much of the "Demon of the Sky" from Echidna mythology. In truth, however, I can find no alternative._

_4/12/49: I have accepted Doom's deal and he gave me a sample of his own blood; it is magenta in color. Well, time to get to work._

_5/21/49: Damn it all to hell and gone! Trying to figure out Doom's D.N.A. is pointless! I have been trying to create a creature with his blood, maybe seeing it in action will tell more about it. I could not make a human, had better luck with Mobians, hedgehog specifically. Even when they survive their creation, the hedgehogs die after just a few moments in the open air of the lab! I am thinking we need to try something more natural. I created some hedgehog sperm from Doom's blood, after a week of trail and error. I approached Doom with this plan and told him that with the age accelerants I had made, the growth from birth to maturity would only take two months. Doom said he could only delay the Black Comet's departure for another month and a half. Still, he seemed pleased with this plan and gave me one of the jewels he wore, a red one. The jewel contained the blood of a warrior princesses Doom once fought, an Echidna to be exact. Just how old is he anyway? Regardless, I created an egg with the blood and artificially impregnated a female hedgehog volunteer. And now we wait._

_6/30/49: Today was very eventful. Our hedgehog volunteer gave birth... to twins. The first one born had black fur and the second had grey. The black one didn't cry when he was born, didn't move, or breath. He was placed on a trey and the doctors returned to the hedgehog volunteer as she birthed the grey one. He came out wailing. Then, while we were all focused on the grey one, the black one woke up and escaped the Delivery Room through a floor vent! Everyone, from solider to scientist, spent the next three hours to try and find him. I was the one to find him, in Maria's room. Apparently, he had found his way to her room and Maria had been taking care of him, even named him! She started call him Shadow, due to his black fur. She refused to give him up, so I let her keep him, after I gave him a shot of Compound 37, which will, hopefully, activate his Black Arms D.N.A. and grant him immortality._

_Shadow... I hope you are what we need._

The next several entries were about Shadow's life aboard the ARK and Maria's decline in health. Most of it Shadow already knew about or could guess what happened. The last entry caught his eye:

_8/5/49: The government has been asking a lot of questions lately. I am beginning to think they do not trust me anymore. I am going to meet with the president tomorrow and, hopefully, straighten everything out. I am so close to a cure for you, Maria, you will see the Earth soon._

Shadow turned off the computer and sighed; he knew how Gerald's meeting with the "president" ended. Still, now he had a better idea of his past; he now knew he had a mother and a twin brother. Could that be Scarlet? The grey hedgehog was never mentioned again in the document; perhaps neglect drove him to hate the brother who took the spotlight? But, Shadow's twin had grey fur, not red fur. Still, Scarlet could change the color of his fur.

The dark hedgehog left Gerald's office and resumed his walk through the halls of the ARK, convinced there was more to find.

* * *

Shadow took a sip of the tea Rouge made them. "Thank you, Rouge." he said.

"You're welcome." said the bat. She sighed and asked, "Shadow, what are you going to do?"

The ebony hedgehog closed his glowing eyes. "Keep running, I guess."

Rouge placed her hand on his shoulder. "Well, you can always count on me."

Shadow put his tea cup down and embraced the bat. "Thank you some much, Rouge."

The huntress returned the hug.

"I'm sure Shadow would be glad to know you're so loyal to him."

Rouge backed out of the hug. "What did you say?"

A wicked grin appeared on the hedgehog's face as he changed into; his fur turned red, his streaks turned black and the patch of fur on his chest turned yellow.

Rouge stood up and back away from the hedgehog. "Who are?"

"Just a guy who loves to have fun," the crimson hedgehog replied and then punched Rouge in the gut, which knocked her out. Scarlet had her bound and gaged before she hit the ground. He then activated the communicator in his left glove. "Doctor." said Scarlet into the communicator.

The all too familiar voice of Dr. Eggman came from the communicator and said "How's the mission going, Scarlet?"

"Phase One is complete; Sonic is no more. Phase Two is also complete; Shadow has been framed for his murder and is being chased by G.U.N. and I've just completed Phase Three; Rouge has been captured."

The deranged doctor let out an evil laugh. "An excellent job Scarlet, now bring Rouge to our mountain camp so we can began Phase Four."

"On my way." Scarlet turned off his communicator and turned his attention to the unconscious bat at his feet. His wicked grin returned as he said, "I don't see why I can't have fun with you first."


	5. Quick Announcement

**Quick Announcement:**

Those of you who do not follow all of my stories maybe unaware of recent events, namely my intention to edit and complete all of my currently "in progress" stories, starting with _Shadow Ends It,_ followed by _Shadow the Hedgehog 2_ and then _The Shadow of Choas_. This announcement is simply to bring you up to speed.

~DisjointWinter

P.S. When the next chapter comes out, I will replace this announcement with it. Any reviews for this chapter will remain, even if I delete this first, so do not review here until it has been posted.


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